Missing Areas

Although there exist remnants of a debug menu in the game, we still don't know how to access it... so for now, I hope you enjoy dicking about with Cheat Engine! Or you can use these VisualBoyAdvance savestates in the US ROM.
(if anyone has the know-how to make convenient GameShark codes out of this, be my guest!)

You'll want to find the address that determines what area you're in (it usually ends in CD38?). It increases by 36 for every new area, and by 80 between every mission, though it's easiest just inputting one of the values below in the appropriate area, that'll get it for sure.

The new area will only be loaded when you leave a screen, begin a mission or continue from a game over. Continuing seems to be the most reliable method, as entering from the mission select may take you to Mission 1, no matter what the value was.

ｶｲﾊﾂ ﾃｽﾄ1 is an original area constructed from Mission 5's assets, and serves as a room for testing weapons and recording their damage. A large white/red blinking circle floats in front of the player and will absorb all damage, displaying what damage the attack does at the top right corner.
The items in order are Heavy Machine Gun, Shotgun, Rocket Launcher, Flame Shot, Laser, Iron Lizard, Enemy Chaser, Super Grenade, Drop Shot, Fire Bomb, Grenade, extra ammo and extra bombs.
However, without a proper level select command, you can't actually take these weapons anywhere. The doors at the end can't be entered either.

ｶｲﾊﾂ ﾃｽﾄ2 is assumedly a vehicle testing area. It's a room with a sole squid occupying it and lots of irregular platforms to test the Metal Slug's traction. The doors at the far left will lead you to Mission 1's third area.

A straight copy of Mission 5 route 3 area 3, this crams as many vehicular enemies as it can in... often so much so that some enemies don't load unless you backtrack. The missile launchers seem to fire several dozen missiles at once. There is no exit.

The five other test stages appear to be straight copies of the areas they take place in. Whether the demos were coded at all is unknown.

3-07

The first of two unused underwater areas!

As touted in the early footage, the game was to include undersea segments where you would pilot the Slug Mariner, but all evidence of this was cut from the game (but not the boxart)... which was easy, given how they were little more than alternate paths. You spawn in these areas on foot; as of yet, I haven't found a way of accessing the Slug Mariner itself, if it was ever completed.

This area is populated only by sea mines and a couple of rocks, both unused objects. There are no prisoners or hidden hot spots.
The mines behave as you'd expect them to, bobbing around and detonating if the player touches them; they will inch forward a little bit if the player is in range.
The rocks were to be roadblocks you'd need to destroy, but they only detect weapons, not players; you're free to walk through them without a care. They can be destroyed, but merely disappear without debris or sound effects.

Exiting to the right will lead you to area 3-09.

3-08

The entrance point to the Slug Mariner in Mission 3. It isn't there, though, and jumping in the water will kill you. Going left, however...

... will enter you from the bottom-right of the second area, where you'll also fall off the screen and die. It's clear this was to be an alternate path, but was sealed up with that wall. The sneaky devils.

3-09

The exiting point from the Slug Mariner. Going right will take you straight to the boss.
As far as I'm aware, those water tiles go unused as well; they're different from the ones you'd see in the last area of Mission 3.

4-05

The boarding point for the Slug Mariner in Mission 4. Same deal as last time. Going left...

... will dump you out below Prisoner 050, in the bottom-right of the second area. Yet another alternate path scrapped not even by walling it off, but by simply removing the exit code. Without this path, your only incentive to visit this area is to rescue two prisoners and get a Shotgun.

4-06

The second unused underwater area! This one is quite vertical, so it's recommended you use the moonjump code to navigate.

Alongside the mines, this area introduces the unused squid enemies, using them during the vertical ascent in a manner similar to the giant eels in Metal Slug 3's first mission. They ordinarily swim through leisurely, but will turn red and zoom forward if the player gets too close. Although their hitbox is a little quirky (are they harmless until turned red?), they function perfectly fine.

Exiting this area will deposit you in area 3 from the same entrance as you would playing normally. However, there's an unused entrance that will spawn you at the bottom-left (best accessed by going right in room 6-40 and setting the level warp value to 4-03), where there's a convenient patch of water. It'll dunk you in the drink and kill you instantly, natch, but it's another clue towards the scrubbing of these alternate paths, leaving now-pointless chunks of level design.